Tif image reading Error

KNIME Extensions Image Processing
#1

Dear Developer

I am using KNIME 3.1.2 and I have problem by reading Tiff image acquired by Olympus microscope. When i try to read it by Image reader an error message appear (Encountered errors during execution!).

 

Thanks in advance

Mohanad Shukur

#2

Hi Shukur, thank you for reporting this bug!

Sadly I could not reproduce the bug with your image, could you please provide is with the following information to allow us to investigate the cause of the bug:

- What operating system are you using?

- Do you have the nightly update site installed?

- Can you please attach the KNIME log from after your tried to run the node? To do this just got to View -> Show KNIME log in the menu of KNIME. Just copy the whole file and attach it to the post.

best 

Gabriel

#3

Dear Gabriel

Thanks for quick answer

I am using Windows 7 professional

I dont know if I installed the nightly update site correctly (can you give some guidness)

this is the log

 

#4

Hi Shukur,

If you are using the nightly build, updating KNIME might be enough to solve your problem. We have fixed several bugs with the image reader in the last days, your error is most likely  one of them.

Regarding the nightly update site, take a look at this guide:

https://tech.knime.org/wiki/knime-image-processing-nightly-build

best,

Gabriel

#5

Dear Ms. Gabriel

I asked you before monthes about my problem reading tiff image by KNIME softwar and you kindly guid me through it. I am really sorry for late replay on your answer, but the problem was not totally solved. I figured out that the error was in the image it self, in which the camera fixed to the microscope take 12 bit image. Both ImageJ or Cellprofiler read the Image as 16 bit, but this is not the case with KNIME. So now I convert the image to 16 bit by cellprofiler pipeline and then use it by  KNIME. Now everythings is working well, but I have two questions:

1. Is it possible to convert the image from 12bit to 16bit, or reading and processing it directly in KNIME instead of using other software?

2. What is the best way to convert it without loosing the data?

Thanks for your help

Mohanad

#6

Hi Shukur,

You should be able to read all the images you can read with ImageJ in KNIME. KNIP does support 12-bit images so this is a curious case, thank you for reporting it.

Is it possible for you to send me a different 12bit example file? I can not reproduce the bug with file you posted at the beginning of the thread, as it works with the latest KNIME + KNIP version.

best,

Gabriel

#7

Dear Ms. Gabriel

Thanks for replay. I upload hier original images of 12 bit and some 16 image converted by ImageJ.

Note: each image is about 2.6 Mb, if you need more images is it possible to send it to you by email, because the formum not support file exced 4 MB and not support TIFF files.. So its not easy to compress every one and send it alone.

Best wihes

Mohanad

#8

Hi Mohanad,

I created a workflow that allows you to read the 12bit, which are stored as 16 bit images, and convert them to Unsigned12BitType images. The conversion is free from loss of information, so you should be able to use the images in your research without any problems.

#9

Dear Gabriel

I am very thankful for your help to creat this flow. Its working well with modified Image (16 bit).

Then if I got it in right way, its not possible for KNIME to read my images directly without saving first as 16bit image by other software like ImageJ or Cellprofiler, then process the resulted image with knime?

 

Thanks once again

Mohanad

#10

Hi Mohanad,

I tested the workflow with the file contained in your

 example. I understood those are the unmodified files. If you have other files which can not be read by KNIME can you please post them so I can investigate it?

best

Gabriel